Cure for Aging Can Be Created Using Directed Evolution

Project description:

Accumulating evidence suggests that microbiota plays an important role in modulating lifespan. This makes possible to use symbiotic bacteria as “living drugs”, which live in the host organism and promote its longevity. We propose to create bacteria, which dramatically extend lifespan of its host. Such bacteria have to produce not one, but a set of longevity-promoting substances with optimal concentrations and dynamics of secretion. To obtain such bacteria we propose to use directed evolution, a process that mimics Darwinian selection on a laboratory scale. This approach has never been applied to drug development before. Directed evolution enables simultaneous modulation of a number of bacterial metabolic pathways andsubsequent selection of the most effective longevity-promoting variants. Experiments will be conducted on a model system consisting of C.elegans and its intestinal symbiont E.coli. Due to highly conserved aging pathways, obtained bacteria may be further used to develop longevity-promoting human drug.

Bacteria E.coli serve as the food source for C.elegans, but at particular stages of the nematode life course they can also exist as intestinal symbionts. Moreover, it was shown that E.coli influence physiology and lifespan of C.elegans. It was revealed that several mutations in E.coli genome increase or vice versa reduce the nematode lifespan.

Symbiont 1

The relationship between C.elegans and E.coli at different stages of the life course of the nematode

Left picture – During development, bacteria mainly serve as a source of food for C.elegans

Center picture – In adult worms some bacteria are not digested and become symbionts

Right picture – As the worm ages, bacteria proliferating within the lumen of the gut become detrimental to the host (Cabriero and Gems, 2013)

The project aims to create E.coli strains that are able to extend the lifespan of C.elegans. For this purpose we propose to employ directed evolution – a process that mimics Darwinian selection on a laboratory scale. At first, phenotypic diversity of E.coli is generated using global transcription machinery engineering (gTME) approach. The gTME randomly alters key proteins regulating the global transcriptome and generates a new type of diversity at the transcriptional level. Then a set of bacterial strains with reprogrammed transcriptome (a bacterial library) is created and E.coli strains which demonstrate the highest ability to extend C.elegans lifespan are selected. We propose to perform not less than 2 cycles of gTME.

For gTME we propose to alter genes of transcription initiation factors σ, which regulate expression of hundreds of genes. At the first cycle of gTME the gene which encodes the main sigma factor σ70 (RpoD) is subjected to random mutagenesis. At the second cycle of gTME the gene of sigma factor σ38 (RpoS), which regulates expression of stationary phase genes, is targeted for mutation.

The selected bacteria are studied to identify transcriptome, proteome and metabolome modifications which result in longevity-promoting phenotype.

Research goal:

Creation of symbiotic bacteria, which are able to increase the lifespan of the host, and study of biological mechanisms underlying these longevity-promoting interactions.

Symbiont 2Research plan

I stage – Creation of bacterial strains which extend the lifespan of C.elegans

(duration – 1,5 years)

1) Construction of library of E.coli strains with reprogrammed transcriptome

- Random mutagenesis of σ-factor gene using error-prone PCR.

- Cloning of obtained sequences into plasmids and transformation into E.coli.

2) Selection of E.coli strains which demonstrate the highest ability to extend C.elegans lifespan

- C.elegans are raised on one of the bacterial mutant strains and analyzed for their lifetime. 1500-2000 strains from mutant library are screened.

- Selection of E.coli strains which demonstrate the highest ability to extend C.elegans lifespan.

2nd cycle of gTME using the gene of another σ-factor – iteration of experiments 1)-2)

II Stage – Study of E.coli strains which extend the lifespan of C.elegans

(duration – 1 year)

- Analysis of transcriptome, proteome and metabolome of E.coli strains which promote longevity of C.elegans.

- Identification of E.coli genes and biological pathways which affect the lifespan of C.elegans.

Expected results:

  • Development of longevity-promoting “living drug” based on symbiotic bacteria.
  • Demonstration of the possibility of directed evolution to create symbiotic bacteria with such a complex phenotype as ability to extend the host lifespan.
  • Identification of new genes and biological pathways of coli which affect C.elegans longevity.

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Main Mistake of Steve Jobs

picture08

I’m quite fed up with the argument against life extension and physical immortality mentioning Steve Jobs who said that “death is very likely the single best invention of life». It’s actually a form of the Buyer’s Stockholm Syndrome, when a person makes a not necessary and expensive purchase and starts to look for arguments that it’s not too bad after all. Only despair and hopelessness make a person justify death. Death is not the single best invention of life, but the worst thing that can happen in it. The whole essence of life is to struggle against death and fight for survival.

Yes, death emphasizes the beauty of life, but it can well do that in a theoretical sense. Like the worst-case scenario that should be avoided. While people are mortal, a human life is a tragedy. Regardless of what a person was doing in life, everything that they lived for will disappear including them. Only striving to immortality and the infinity of goals make sense. Otherwise one can always put the person at a stand by asking the repeating question “why are you doing this?” and regardless of the answer, ask again “and why is this?” If there is no infinity then the person comes to an unavoidable loss of sense.

My answer is that the meaning of my life is in having a tomorrow. I want every tomorrow to have its own tomorrow. Death is when your tomorrow never comes.

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Longevity Cook Book

Longevity cook book menu draft 1

My colleagues and I would like to launch the Longevity Cook Book crowdfunding campaign in upcoming three months.

We would like to raise fuding to create a book that will tell the story about what longevity depends on, what processes are going on in our bodies during aging and how they can be slowed down, dieting in the right way, based on the current scientific knowledge. The book will contain the most up-to-date research data on the beneficial properties of various foods, their longevity effects and abilities to prevent different age-related diseases.

Longevity Cook Book will give you the special recipes, developed with the help of professional chefs, on how to cook longevity-boosting dishes from the healthiest ingredients possible.

Besides the recipes, the book will tell you how to “cook” longevity in terms of science. I will explain the existing directions in aging research and the most promising experiments that need to be carried out to make a truly long and healthy life a reality.

Here’s the Longevity Cook Book plan:

Part 1

  • The role of diet in health and longevity. I will describe the diets that increase longevity and prevent age-related pathologies (with proof in humans and model animals)
  • Physiology of nutrition. I will explain how food is digested, how the nutrients are absorbed in the intestines, how they enter blood stream, what they do inside the cells. There will be some pretty pictures to illustrate all of that.
  • Brief and easy-to-understand description of aging mechanisms and the mechanisms of age-related pathologies (like cardiovascular diseases, diabetes, etc.) and how diet can influence those mechanisms

Part 2

Description of the healthy foods including scientific papers, illustrating why they are healthy, and biological mechanisms that those foods influence

Part 3

Longevity Menu. Dishes made with longevity foods cooked the healthiest ways accompanied by pretty pictures of the dishes.

Part 4

“Cooking” longevity. I will describe the main approaches to solving the problem of aging and the most promising experiments.

How do you like the idea? Would you be interested in reading such a book?

For the crowdfunding project to be successful it has to have a powerful start, therefore I’d like to agree on reposting the campaign when it launches in advance.

I call upon everybody to, please, let me know, who would be up to spreading the word about this project when the time comes.

If you have some nice amount of people following you on twitter or other social networks, I’ll be happy to collaborate.

I also welcome advice on how to engage a larger audience. Maybe you have some journalists or bloggers that you know?

I present a draft of a possible layout of one of the pages.

There will be many different icons that tell you various bits of information about the dish. In particular on this page a face means the research on the given type of food was done in humans, a mouse – on mice, a test tube – on cell cultures.

We haven’t yet put together the pictures of aging mechanisms, but we will definitely do it.

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Longevity Gene Therapy – Updated Projects

While discussing the longevity gene therapy project we encountered various questions and observations that prompted us to broaden the project and slightly change it. Generally, all the comments can be reduced into 5 main points:

  1. You need to enlarge the list of therapeutic genes by adding to it this and that.
  2. You want to use too many genes; therefore you need to make the project simpler by keeping only the most effective genes
  3. If you apply all the genes at the same time, some of them may cancel out the effects of other genes.
  4. Will it be safe to use viral vectors to deliver genetic constructs?
  5. How safe are therapeutic genes for the body?

Some of the observations were of completely opposite nature, so we decided to do 2 versions of the project. One of them is for aging geneticists. In it we almost double the list of the genes extending lifespan. This project will allow testing many poorly studied genes, but promising in terms of aging. Besides, some unexpected results can be obtained, which is always valuable.

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Popular Lectures on Gene Therapy

We have put together a list of popular science video lectures on gene therapy – one of the most promising molecular medicine directions. What makes this approach different is that nucleic acid molecules, DNA and RNA, are used as therapeutic agents.

To have the most general idea about the principles of gene therapy you can watch this video

The lecture by Dr. Hans-Peter Kiem from Fred Hutchinson Cancer Research Center at University of Washington provides more detailed information about the main approaches utilized by gene therapy, nucleic acid delivery methods into the cells and also the diseases that use gene therapy for treatment

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We Can Learn a Lot from Yeast How to Slow Down Aging

Valter Longo's lecture

Dr. Valter Longo hold the record of yeast lifespan extension. He was able to increase longevity of this species 10 fold. This a one of the most remarkable results in longevity science. Here Dr. Longo is giving us a lecture on yeast genetics. Let me summarize what he told us.

Yeast are unicellular organisms. They have 6,000 genes packed in 16 chromosomes. They divide every 90 minutes. They are one of the widely used model animals for research, and not only aging research, because they are safe, quite easy to handle and inexpensive. One of the best feature for aging research is that their lifespan is really short. I will use a vague term – about a week, because it depends on the way how you measure their longevity.

There are two major methods to see how long yeast live – replicative and chronological lifespan analyses. The first one looks at the dividing mother cell and determines how many times the  division happened. People can distinctly distinguish the newly formed daughter cell and the mother cell, because daughter cells are smaller in size. This work is really tedious, because it relies on manual sorting of the cells. None the less, this is how we can measure the yeast health span – the period of time when the cell is able to give progeny. After it has no more “babies” it doesn’t die though immediately (humans don’t too), however this assay doesn’t include the time when the cell remains alive.

The chronological lifespan analysis looks at how long the non-diving colony of cells live. The number of cells alive at each particular moment is estimated by the number of colonies that they form on a plate with nutrients that allows growth so the colonies can be visible. In order to bring the yeast to a non-diving state, they are stripped of nutrients in the medium, so they switch to a growth arrest state to ensure survival rather than reproduction. This is called a post-diauxic phase. Their survival is approximately 6 days in this state. And the metabolic rates are very high.

One of the ways to extend yeast lifespan is to remove all nutrients from the medium and simply substitute it with water. They will then enter a stationary phase when their metabolic rate is reduced, which allows better stress resistance and longer survival, about 17 days.

There is an even great lifespan extension mode that allow yeast cells live years – spore state. If you put the cells in 1% potassium acetate, the cells will convert into spores and will be able to live several year. They will be dormant and highly stress resistant. I can’t say anything about their metabolic rate though, and do you know why? Because nobody in the world in studying that. Can you believe it? I was so surprised. The reason why is I guess because of lack of funding. So, there is no person or agency in the world that is interesting in learning how an organism that normally lives just 6 days can manage to stay alive for several years. This is just so hard to grasp for me.

In yeast the best gene found so far for longevity interventions is Sch9. It is an analog of the S6 kinase that mammalian cells have to sense nutrients and respond in growth and division. Sch9 is more central in nutrient signaling than tor1. This is probably true for all eukaryotes. We know interventions for mTOR, which is a drug that suppresses mTOR activity, called rapamycin. Apparently, there maybe even more potent drugs that slow down aging that work on the S6 kinase. They haven’t been identified yet.

Another very interesting genes in yeast is rash. It senses glucose. Mutant yeast that don’t have this gene also live longer, but not as long as the “top record holder” Sch9 mutants. Sch9 can be seen as a conductor that orchestrates what is happening in the cell. I loved this beautiful analogy that Dr. Longo used, because it really makes you understand why sometimes if a trumpet plays really loud (and a trumpet is a very nice instrument), the whole orchestra doesn’t sound better. It’s the same when you activate one thing, one very good thing on its own, but all together you don;t see an improvement in life extension. The reason is because you need to influence the “conductor”, a gene like Sch9 in yeast.

Sch9 operates through msn2 and msn4 genes that pass on the orders of the “conductor” and activate various genes like cytoplasmic catalase T (anti-oxidative stress gene), DNA damage response genes, heat shock protein 12, trehalose phosphate phosphatase (stress protectant) and others. Also MnSOD (superoxide dismutase, anti-oxidant enzyme) is required for the longevity effect of switching off Sch9 to take place. This effect is 3 times lifespan extension, by the way. Over expressing SOD can only give 10-30% lifespan extension, so it’s crucial when it works together with the “conductor”.

Mutations in tor1 and school that delay aging cause a metabolic shift from the catabolism of glucose and ethanol to respiration and production of glycerol. Glycerol for yeast appears to be a neutral carbon course that does not promote pro-aging phenotype. It’s kind of like “good fat”, like olive oil. Mitochondrial superoxide is a major mediator of DNA mutations, aging, death, and the release of nutrients. Mutations in the Sch9 or Ras pathways extend life span in part by increasing protection against mitochondrial superoxide.

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Fund Anti-Cancer Research and Make Drugs Cheaper at the Same Time

This is a very cool crowdfunding campaign – you can help create a new cancer drug and at the same make it much cheaper. How? The researchers will not patent the drugs. Like polio vaccine, which was never patented, therefore it was widely available. Check out the website and the video. I loved it and made a donation of $50, because I find projects like this can change the existing paradigm in healthcare when the existing drugs are just deadly expensive. I encourage you to support the project and share it with your friends.

By the way, in aging there are also drugs that can never be patented like aspirin, metformin and rapamycin, but may well extend our lifespan. No pharmaceutical company will be interested in looking at substances that can’t be patented, but this could make our lives longer and healthier.

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